openfold issues

Cannot Run Structure Prediction – Missing Modules

1

## ❗Issue Summary I want to use OpenFold for local protein structure prediction (no training), but none of the commits (including `main` and `v2.1.0`) seem to be fully functional. Specifically:...

373375458

Deepspeed evoformer attention bfloat16 consistency issue

We have observed a few issues with the deepspeed evoformer attention for bfloat16. In particular: - The unit test [`TestDeepSpeedKernel.test_compare_model`](https://github.com/aqlaboratory/openfold/blob/main/tests/test_deepspeed_evo_attention.py#L278) in `tests/test_deepspeed_evo_attention.py` fails 30-50% of the time when the precision...

jnwei

FileNotFoundError

1

Hello, We are encountering an error when attempting to run OpenFold on our cluster to predict the structure of a dimer. The job fails with the following `FileNotFoundError`: ```{bash} Traceback...

marctormo

Feat/cyclic offset

# Description The purpose of the PR is to implement the cyclic offset positional encoding in OpenFold. Currently, the residue relative positions are computed linearly, meaning that the sequence is...

ioannisa92

How to run for solo sequence without template

I want to run for a single sequence and do not want to use template and the following is what documentaion says but when I run by just giveing the...

nobleaustine

Explicitly set reentrant to `False` for torch checkpointing

1

## Description The purpose of this PR is to set up OpenFold to be compatible with torch 2.6 (technically >=2.4), in particular for using `torch.compile` on modules that do activation...

an1lam